I could really use some help figuring out the best way to set up ballast in my Gekko (GTS-20), I recently started entering wakeboard comps and they use Tiges and X-Stars so I need to amp up my boat's wake for practice. I'm also trying to figure out a good set up for surfing.

Any one on here have experience with this (or a similar) boat? I have two fat sacs currently, one 500lb and one, i think, 300 lb. I've tried a bunch of different ways (both bags in back, one in back one in front, either side of the engine) it seems like putting the bags on either side, with the larger one only partially full, works pretty well for wakeboarding. The wake does get a little lippy but a lot better than before so we were thinking about getting two bags to keep under the floor all season, however we wouldn't be able to empty them- they would have to stay full which I know probably isn't the best for the bags. Any ideas about how we could keep the water from getting stagnant and moldy for few months (chlorine tabs or something?) or other ways to have ballast underneath without installing an expensive system?

As for the surfing, we haven't been able to get the wave quite right- its too high and the pocket is too short. I think I need more weight to the front of the boat but there's not really any room for ballast towards the front.

Your boat is really low so I would not leave the ballast full.
I would try to get another sac the same as your 500 and run one on either side of the engine. Move them back a bit to steepen the wake or forward to get rid of froth on top of the lip. You could then try moving them back some and adding the 300 in the bow area, or forward some and using the 300 in the rear ski locker or floor. You may find it useful to reprop if you are running 1000# in the boat but do that after you get the wake sorted.
For surfing, find a way to put that 300 under the bow on the side you want to ride. If the pocket is still too short move people forward as much as you can but keep the boat with a lot of list to the side you're surfing.
It is possible to add lead or steel shot in the bow easily and many do that. I, personally, would never do that with very much weight.
Caveat - I have not ridden in a Gekko like yours, so I might be totally wrong.

I've seen the revo 6.7 loaded down to about 6000# (boat plus ballast). The wake just doesnt get that big because its a ski boat and the hull provides too much lift to push the water around. The wakesurfing wave was decent on the drivers side.

When I had a GTS20 I put a 500lbs bag on each side of the engine as far forward as you can and if you want, you could put that 300lbs bag in the rear, just remove the seat. That should make a real nice wake. Just remember to bump the throttle a little when almost stopped so you don't get water coming in over the back of the boat.
You will not get very much weight under the floor of that boat, there just isn't room.
I have no experience with the wakesurf setup on a GTS.